title: High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.
abstract: A key prerequisite to understand how gene regulatory processes are controlled by the interplay of RNA-binding proteins and ribonucleoprotein complexes with RNAs is the generation of comprehensive high-resolution maps of protein-RNA interactions. Recent advances in next-generation sequencing technology accelerated the development of various crosslinking and immunoprecipitation (CLIP) approaches to broadly identify RNA regions contacted by RNA-binding proteins. However these methods only consider single RNA-binding proteins and their contact sites, irrespective of the overall cis-regulatory sequence space contacted by other RNA interacting factors. Here we describe the application of protein occupancy profiling, a novel approach that globally displays the RNA contact sites of the poly(A)+ RNA-bound proteome. Protein occupancy profiling enables the generation of transcriptome-wide maps of protein-RNA interactions on polyadenylated transcripts and narrows the sequence search space for transcript regions involved in cis-regulation of gene expression in response to internal or external stimuli, altered cellular programs or disease.
authors.affiliation: Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle Str. 10, 13125 Berlin, Germany.
authors.forename: Mathias
authors.initials: M
authors.lastname: Munschauer
authors.affiliation: Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle Str. 10, 13125 Berlin, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Schueler
authors.affiliation: Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle Str. 10, 13125 Berlin, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Dieterich
authors.affiliation: Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle Str. 10, 13125 Berlin, Germany. Electronic address: markus.landthaler@mdc-berlin.de.
authors.forename: Markus
authors.initials: M
authors.lastname: Landthaler
mesh_terms: D000818:Animals; D001665:Binding Sites; D045744:Cell Line, Tumor; D053595:Embryonic Stem Cells / Q000737:chemistry / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D015723:Gene Library; D061307:Human Umbilical Vein Endothelial Cells / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D051379:Mice; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020543:Proteome; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
keywords: CLIP; Next-generation sequencing; Non-coding RNA; PAR-CLIP; Protein occupancy profiling; Protein–RNA interaction; RNA-binding protein; lincRNA; mRNA